1-11497869-T-G

Variant names:

• chr1-11497869-T-G
• rs4846012
• NM_020780.2:c.-3-3121T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020780.2(DISP3):​c.-3-3121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,162 control chromosomes in the GnomAD database, including 20,551 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (20551 hom., cov: 32)
• Consequence: DISP3 NM_020780.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

DISP3 (HGNC:29251): (dispatched RND transporter family member 3) Involved in negative regulation of neuron differentiation; positive regulation of lipid metabolic process; and positive regulation of neural precursor cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC124903842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISP3	NM_020780.2	c.-3-3121T>G		intron_variant	Intron 1 of 20	ENST00000294484.7	NP_065831.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISP3	ENST00000294484.7	c.-3-3121T>G		intron_variant	Intron 1 of 20	1	NM_020780.2	ENSP00000294484.6

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71589 AN: 152042 Hom.: 20546 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 71601 AN: 152162 Hom.: 20551 Cov.: 32 AF XY: 0.467 AC XY: 34745 AN XY: 74372

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.487

Alfa AF: 0.568 Hom.: 10841

Bravo AF: 0.458

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4846012; hg19: chr1-11557926; COSMIC: COSV53823718;